14-20457358-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001641.4(APEX1):c.807T>A(p.Tyr269*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,614,122 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001641.4 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
APEX1 | NM_001641.4 | c.807T>A | p.Tyr269* | stop_gained | Exon 5 of 5 | ENST00000216714.8 | NP_001632.2 | |
APEX1 | NM_001244249.2 | c.807T>A | p.Tyr269* | stop_gained | Exon 5 of 5 | NP_001231178.1 | ||
APEX1 | NM_080648.3 | c.807T>A | p.Tyr269* | stop_gained | Exon 5 of 5 | NP_542379.1 | ||
APEX1 | NM_080649.3 | c.807T>A | p.Tyr269* | stop_gained | Exon 5 of 5 | NP_542380.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152230Hom.: 0 Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461892Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 727246
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152230Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74378
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at